Supplemental files for manuscript entitled 'A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians'

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dc.contributor.affiliationUniversity of Helsinki-Dunn, Cory D.
dc.contributor.authorDunn, Cory D.
dc.date.accessioned2025-04-29T13:59:28Z
dc.date.issued2021-04-30
dc.date.issued2021-04-30
dc.descriptionSupplemental files for the manuscript 'A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians'. Supplemental File 1: All predicted protein substitutions along all edges at positions containing less than 2% gaps across input and ancestral sequences are listed, along with associated inferred taxonomy information, TSS, and branch length. All alignment positions refer to the Bos taurus reference sequences.   Supplemental File 2: The TSS value calculated for each mitochondrial protein alignment position using the mammalian reference sequence dataset is provided. All alignment positions refer to the Bos taurus reference sequences.   Supplemental File 3: SPCS and θevo outputs are provided for analyses across all mitochondria-encoded positions, as well as for focused analyses of specific OXPHOS complexes and individual proteins.   Supplemental File 4: A GenBank flat file containing RefSeq entries for mammalian mtDNAs and the entry for the reptile Anolis punctatus.   Supplemental File 5: A maximum likelihood inferred tree generated by RAxML-NG analysis of concatenated and aligned protein coding sequences from mammalian and Anolis punctatus mtDNAs.   Supplemental File 6: Bootstrap replicates were generated from the alignment of concatenated protein coding sequences. Felsenstein’s Bootstrap Proportions (Felsenstein 1985) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.   Supplemental File 7: Bootstrap replicates were generated using concatenated mammalian mtDNA coding sequences. Transfer Bootstrap Expectations (Lemoine et al. 2018) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs. Supplemental File 8: PAGAN tree output using aligned amino acid sequences and the rooted maximum likelihood inferred tree as input.
dc.identifierhttps://doi.org/10.5281/zenodo.4729143
dc.identifier.urihttps://datakatalogi.helsinki.fi/handle/123456789/4288
dc.rights.licensecc-by-4.0
dc.subjectbioenergetics
dc.subjectmolecular evolution
dc.subjectmitochondrial DNA
dc.subjectprimate evolution
dc.subjectprotein structure and selection
dc.subjectmammal biology
dc.titleSupplemental files for manuscript entitled 'A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians'
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